.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
.TH SLICE_MERCATOR_ALIGNMENT "1" "December 2015" "slice_mercator_alignment 1.15.9" "User Commands"
.SH NAME
slice_mercator_alignment \- Extracts the corresponding subalignment from a Mercator multiple alignment
.SH SYNOPSIS
.B slice_mercator_alignment
[\fI\,options\/\fR] \fI\,<genome> <chromosome> <start> <end> <strand>\/\fR
.SH DESCRIPTION
slice_mercator_alignment from FSA 1.15.9
.PP
Extracts the corresponding subalignment from a Mercator multiple alignment.
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-\-help\fR
show this message
.TP
\fB\-D\fR, \fB\-\-data\fR <directory>
path to map, genome and alignment files
.TP
\fB\-M\fR, \fB\-\-map\fR <directory>
path to map and genome files
.TP
\fB\-A\fR, \fB\-\-align\fR <directory>
path to alignment files
.TP
\fB\-L\fR, \fB\-\-lazy\fR
warn, rather than die, if the subalignment can't be obtained
.TP
\fB\-U\fR, \fB\-\-truncate\fR
truncate unmappable sequence (rather than skipping) and show truncated subalignment
.TP
\fB\-s\fR, \fB\-\-stockholm\fR
use and display Stockholm\-format alignments with conservation statistics (default is multi\-FASTA)
.TP
\fB\-0\fR, \fB\-\-zerobased\fR
coordinates are 0\-based (default is 1\-based)
.TP
\fB\-o\fR, \fB\-\-halfopen\fR
end coordinate is open, i.e., [start, end)
.PP
Assumes that coordinates are 1\-based and fully\-closed,
therefore representing the interval [start, end].
.PP
If requested, unmappable sequence will be truncated to the mappable portion;
note that the truncation will favor the beginning of the requested sequence.
.PP
If the requested sequence is on the \- strand, then the corresponding
subalignment will be reverse\-complemented.
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.